AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380015847.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015847.01.T01 MTR_3g078590 100.000 90 0 0 1 90 1 90 2.67e-63 186
MsG0380015847.01.T01 MTR_3g085890 69.318 88 27 0 1 88 1 88 1.73e-43 136
MsG0380015847.01.T01 MTR_8g080060 69.318 88 27 0 1 88 1 88 4.21e-43 135
MsG0380015847.01.T01 MTR_7g016060 51.220 82 40 0 5 86 3 84 3.60e-29 100
MsG0380015847.01.T01 MTR_3g085890 63.934 61 22 0 27 87 1 61 1.87e-25 90.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015847.01.T01 AT3G48140 74.118 85 22 0 4 88 3 87 1.31e-44 139
MsG0380015847.01.T01 AT3G29970 51.220 82 40 0 5 86 3 84 8.38e-30 101
MsG0380015847.01.T01 AT3G29970 47.059 68 36 0 18 85 1 68 2.33e-20 77.4
MsG0380015847.01.T01 AT3G29970 47.059 68 36 0 18 85 1 68 2.33e-20 77.4

Find 49 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTATTATTGTCATGCATTT+AGG 0.207950 3:-75814674 MsG0380015847.01.T01:three_prime_UTR
AAGTCGCAACTAAGTTGTTT+TGG 0.340325 3:-75814754 MsG0380015847.01.T01:exon
AAACATCAGTACCTGACTTC+AGG 0.347160 3:+75815790 None:intergenic
CCACAGCATACACGCTGTTC+AGG 0.369876 3:+75814625 None:intergenic
AAAGTTACTTCTAGGGAAAC+TGG 0.375628 3:-75814489 MsG0380015847.01.T01:three_prime_UTR
CAACAATTAACGCAACAAAC+AGG 0.381334 3:+75814586 None:intergenic
CTCTTCAACCTTGATGATCT+AGG 0.393617 3:+75814524 None:intergenic
TACCCTCTGTTTGCTGCGGT+TGG 0.396092 3:-75815865 MsG0380015847.01.T01:CDS
AGTTTATTTATTCTTACAAA+TGG 0.404953 3:+75816129 None:intergenic
CTGCGGTTGGAGCTGCTGTT+GGG 0.406881 3:-75815852 MsG0380015847.01.T01:CDS
GCTGCGGTTGGAGCTGCTGT+TGG 0.426937 3:-75815853 MsG0380015847.01.T01:CDS
TATAAATTTGTTCGGTGTGC+CGG 0.440486 3:-75814554 MsG0380015847.01.T01:three_prime_UTR
GCAGACATGCTTGTTAAAAC+TGG 0.453798 3:-75814430 MsG0380015847.01.T01:three_prime_UTR
GTTGAGGCCGGGCATAATCT+CGG 0.455438 3:+75814794 None:intergenic
AACATCAGTACCTGACTTCA+GGG 0.462667 3:+75815791 None:intergenic
AACAAGCAGTCTCGAGCTGC+AGG 0.464020 3:-75814891 MsG0380015847.01.T01:CDS
AGTGAAGAAGCTGTTGAGGC+CGG 0.469984 3:+75814782 None:intergenic
TCTTCTTCAACTGCTATCCA+TGG 0.475644 3:-75816002 MsG0380015847.01.T01:exon
ATAAATTTGTGATGTTGTCT+AGG 0.477019 3:-75814458 MsG0380015847.01.T01:three_prime_UTR
TTTCAACAAAGTTACTTCTA+GGG 0.478418 3:-75814496 MsG0380015847.01.T01:three_prime_UTR
TTGAGGCCGGGCATAATCTC+GGG 0.481836 3:+75814795 None:intergenic
GTCTCGAGCTGCAGGAGTGT+TGG 0.483795 3:-75814883 MsG0380015847.01.T01:CDS
GATTGCAATTTGCAATGGAA+TGG 0.501934 3:+75816061 None:intergenic
AATTTGCAATGGAATGGAAA+TGG 0.511319 3:+75816067 None:intergenic
GGGTCTGATCCAGCGATTGG+TGG 0.513757 3:+75815979 None:intergenic
TTCTGTGTACTTCTCTCCCT+CGG 0.519035 3:+75814851 None:intergenic
CTCGGGTCTGATCCAGCGAT+TGG 0.519677 3:+75815976 None:intergenic
GTGAAGAAGCTGTTGAGGCC+GGG 0.521542 3:+75814783 None:intergenic
TATCCATGGCCACCAATCGC+TGG 0.522115 3:-75815988 MsG0380015847.01.T01:exon
AAAACAACTTAGTTGCGACT+TGG 0.523588 3:+75814756 None:intergenic
TCTGCATCAACCCTGAAGTC+AGG 0.524860 3:-75815801 MsG0380015847.01.T01:intron
TCTCTGAGAGAGAAAGAGAA+TGG 0.528506 3:+75816090 None:intergenic
AAACAACTTAGTTGCGACTT+GGG 0.529015 3:+75814757 None:intergenic
AAGATGATTGCAATTTGCAA+TGG 0.529414 3:+75816056 None:intergenic
AGATCACCCGAGATTATGCC+CGG 0.535231 3:-75814801 MsG0380015847.01.T01:CDS
GATGTTACGAACAAGTGAAA+AGG 0.535731 3:+75815822 None:intergenic
TGATGATCTAGGTTCGATAC+CGG 0.576141 3:+75814535 None:intergenic
GATCCAGCGATTGGTGGCCA+TGG 0.584846 3:+75815985 None:intergenic
CTCCAACCGCAGCAAACAGA+GGG 0.612181 3:+75815863 None:intergenic
GTGTTGGAGAACTTTGCCGA+GGG 0.614956 3:-75814867 MsG0380015847.01.T01:CDS
AACAATTAACGCAACAAACA+GGG 0.625184 3:+75814587 None:intergenic
GGTATACCCTCTGTTTGCTG+CGG 0.632424 3:-75815869 MsG0380015847.01.T01:CDS
CCTGAACAGCGTGTATGCTG+TGG 0.641592 3:-75814625 MsG0380015847.01.T01:three_prime_UTR
AGTGTTGGAGAACTTTGCCG+AGG 0.642190 3:-75814868 MsG0380015847.01.T01:CDS
GGTCAGTGAAGAAGCTGTTG+AGG 0.648101 3:+75814778 None:intergenic
GCTCCAACCGCAGCAAACAG+AGG 0.651727 3:+75815862 None:intergenic
GTATCGAACCTAGATCATCA+AGG 0.676860 3:-75814532 MsG0380015847.01.T01:three_prime_UTR
CAATCGCTGGATCAGACCCG+AGG 0.698764 3:-75815975 MsG0380015847.01.T01:intron
AGTACACAGAACATTTGCTG+AGG 0.706764 3:-75814839 MsG0380015847.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGATATTAACAAAATTTAAT+GGG - Chr3:75814953-75814972 MsG0380015847.01.T01:intron 10.0%
!! TAGATATTAACAAAATTTAA+TGG - Chr3:75814952-75814971 MsG0380015847.01.T01:intron 10.0%
!!! ATAAAAATTTTCATTTTCAA+TGG + Chr3:75815483-75815502 None:intergenic 10.0%
!! AGTTTATTTATTCTTACAAA+TGG + Chr3:75814376-75814395 None:intergenic 15.0%
!! ATTAATCTCTAATATCAAAT+AGG + Chr3:75815207-75815226 None:intergenic 15.0%
!! TTAATCTCTAATATCAAATA+GGG + Chr3:75815206-75815225 None:intergenic 15.0%
!!! AGAGATTAATTTTTATTCAT+TGG - Chr3:75815217-75815236 MsG0380015847.01.T01:intron 15.0%
!!! GAAAATGAAAATTTTTATCT+CGG - Chr3:75815485-75815504 MsG0380015847.01.T01:intron 15.0%
!!! GAATATTCCTTTTTTATTTT+TGG - Chr3:75814873-75814892 MsG0380015847.01.T01:CDS 15.0%
!!! TGTAGTTTTATAAATTTGTT+CGG - Chr3:75815940-75815959 MsG0380015847.01.T01:intron 15.0%
!! AAGAAGATAACAAAAACAAA+GGG + Chr3:75814475-75814494 None:intergenic 20.0%
!! AATTAAATAACTCATGTATC+TGG - Chr3:75815028-75815047 MsG0380015847.01.T01:intron 20.0%
!! ACAAATTGTGAAAATTTAAG+CGG + Chr3:75814929-75814948 None:intergenic 20.0%
!! AGGAAAACCAAAAATAAAAA+AGG + Chr3:75814883-75814902 None:intergenic 20.0%
!! CTAATCGGATAATTAATTAA+TGG + Chr3:75814842-75814861 None:intergenic 20.0%
!! GATACATGAGTTATTTAATT+TGG + Chr3:75815028-75815047 None:intergenic 20.0%
!! TATACCTATAACAAAAAAGA+TGG + Chr3:75814619-75814638 None:intergenic 20.0%
!!! GATTAATTTTTATTCATTGG+AGG - Chr3:75815220-75815239 MsG0380015847.01.T01:intron 20.0%
!!! TCCTAAAAATCACTTTTTTA+AGG + Chr3:75815076-75815095 None:intergenic 20.0%
!!! TTGTTGTTTAATTTTTAGCT+AGG - Chr3:75815529-75815548 MsG0380015847.01.T01:intron 20.0%
!!! TTTAATTTTTAGCTAGGATT+TGG - Chr3:75815535-75815554 MsG0380015847.01.T01:intron 20.0%
! AGAAGATAACAAAAACAAAG+GGG + Chr3:75814474-75814493 None:intergenic 25.0%
! AGTATTATTGTCATGCATTT+AGG - Chr3:75815828-75815847 MsG0380015847.01.T01:CDS 25.0%
! ATAAATTTGTGATGTTGTCT+AGG - Chr3:75816044-75816063 MsG0380015847.01.T01:five_prime_UTR 25.0%
! ATTCCATCATGTTTACTAAT+CGG + Chr3:75814857-75814876 None:intergenic 25.0%
! GAAGAAGATAACAAAAACAA+AGG + Chr3:75814476-75814495 None:intergenic 25.0%
! TTTCAACAAAGTTACTTCTA+GGG - Chr3:75816006-75816025 MsG0380015847.01.T01:five_prime_UTR 25.0%
!! ATGTTTGTTTGTTCTTTTGA+TGG - Chr3:75815578-75815597 MsG0380015847.01.T01:intron 25.0%
!! GCCTTAAAAAAGTGATTTTT+AGG - Chr3:75815072-75815091 MsG0380015847.01.T01:intron 25.0%
!! TGTTTGTTTGTTCTTTTGAT+GGG - Chr3:75815579-75815598 MsG0380015847.01.T01:intron 25.0%
!! TTTTCAACAAAGTTACTTCT+AGG - Chr3:75816005-75816024 MsG0380015847.01.T01:exon 25.0%
!!! AATGGTGATTTTAAAGTTGT+TGG - Chr3:75815177-75815196 MsG0380015847.01.T01:intron 25.0%
!!! TGATTGATTTTTCTCTTCTT+TGG - Chr3:75814765-75814784 MsG0380015847.01.T01:CDS 25.0%
!!! TTCACCATCTTTTTTGTTAT+AGG - Chr3:75814612-75814631 MsG0380015847.01.T01:three_prime_UTR 25.0%
!!! TTGTTTTGGATTAATAACAG+TGG - Chr3:75815762-75815781 MsG0380015847.01.T01:intron 25.0%
AACAATTAACGCAACAAACA+GGG + Chr3:75815918-75815937 None:intergenic 30.0%
AAGATGATTGCAATTTGCAA+TGG + Chr3:75814449-75814468 None:intergenic 30.0%
AATTTGCAATGGAATGGAAA+TGG + Chr3:75814438-75814457 None:intergenic 30.0%
ACGAAATGCAAAGTAGTAAA+TGG + Chr3:75814578-75814597 None:intergenic 30.0%
CATCATATCATTTCTCAGAT+AGG + Chr3:75814903-75814922 None:intergenic 30.0%
TATCCGATTAGTAAACATGA+TGG - Chr3:75814851-75814870 MsG0380015847.01.T01:CDS 30.0%
TGAGATATAACTCAAAAGAG+TGG - Chr3:75815296-75815315 MsG0380015847.01.T01:intron 30.0%
! TTTTATCTCGGTTTTACACA+GGG - Chr3:75815497-75815516 MsG0380015847.01.T01:intron 30.0%
! TTTTTATCTCGGTTTTACAC+AGG - Chr3:75815496-75815515 MsG0380015847.01.T01:intron 30.0%
!!! TTGTTCTTTTGATGGGTTTA+GGG - Chr3:75815586-75815605 MsG0380015847.01.T01:intron 30.0%
!!! TTTGTTCTTTTGATGGGTTT+AGG - Chr3:75815585-75815604 MsG0380015847.01.T01:intron 30.0%
AAAACAACTTAGTTGCGACT+TGG + Chr3:75815749-75815768 None:intergenic 35.0%
AAACAACTTAGTTGCGACTT+GGG + Chr3:75815748-75815767 None:intergenic 35.0%
AAATCCATGATATGTTTGCC+TGG - Chr3:75815386-75815405 MsG0380015847.01.T01:intron 35.0%
ACTCATGTATCTGGACTAAA+TGG - Chr3:75815037-75815056 MsG0380015847.01.T01:intron 35.0%
CAACAATTAACGCAACAAAC+AGG + Chr3:75815919-75815938 None:intergenic 35.0%
GACAAATCAGCTTCAATCAT+CGG + Chr3:75815121-75815140 None:intergenic 35.0%
GATGTTACGAACAAGTGAAA+AGG + Chr3:75814683-75814702 None:intergenic 35.0%
GATTGCAATTTGCAATGGAA+TGG + Chr3:75814444-75814463 None:intergenic 35.0%
TGCATTTCGTAAGAGAGTTA+GGG - Chr3:75814588-75814607 MsG0380015847.01.T01:three_prime_UTR 35.0%
TGGCAAAATACAGATCGAAA+AGG + Chr3:75814558-75814577 None:intergenic 35.0%
TTGCATTTCGTAAGAGAGTT+AGG - Chr3:75814587-75814606 MsG0380015847.01.T01:three_prime_UTR 35.0%
TTTGCACAAATAACGTGGAA+TGG - Chr3:75815159-75815178 MsG0380015847.01.T01:intron 35.0%
! AAAGTTACTTCTAGGGAAAC+TGG - Chr3:75816013-75816032 MsG0380015847.01.T01:five_prime_UTR 35.0%
! AAGTCGCAACTAAGTTGTTT+TGG - Chr3:75815748-75815767 MsG0380015847.01.T01:intron 35.0%
! CGAATTTTGCACAAATAACG+TGG - Chr3:75815154-75815173 MsG0380015847.01.T01:intron 35.0%
! GAGTTTGACTTATCTCAGAT+CGG - Chr3:75814787-75814806 MsG0380015847.01.T01:CDS 35.0%
! TGGTGTTTGAAGGAGTATAA+TGG - Chr3:75815555-75815574 MsG0380015847.01.T01:intron 35.0%
!! TATAAATTTGTTCGGTGTGC+CGG - Chr3:75815948-75815967 MsG0380015847.01.T01:intron 35.0%
AAACATCAGTACCTGACTTC+AGG + Chr3:75814715-75814734 None:intergenic 40.0%
AACATCAGTACCTGACTTCA+GGG + Chr3:75814714-75814733 None:intergenic 40.0%
AACTCAAAAGAGTGGCATCA+TGG - Chr3:75815304-75815323 MsG0380015847.01.T01:intron 40.0%
CTGGTTGAGTGAAATGAAGT+CGG - Chr3:75815405-75815424 MsG0380015847.01.T01:intron 40.0%
GTATCGAACCTAGATCATCA+AGG - Chr3:75815970-75815989 MsG0380015847.01.T01:intron 40.0%
TCAACCAGGCAAACATATCA+TGG + Chr3:75815393-75815412 None:intergenic 40.0%
TCTTCTTCAACTGCTATCCA+TGG - Chr3:75814500-75814519 MsG0380015847.01.T01:three_prime_UTR 40.0%
TGATGATCTAGGTTCGATAC+CGG + Chr3:75815970-75815989 None:intergenic 40.0%
! AGTACACAGAACATTTGCTG+AGG - Chr3:75815663-75815682 MsG0380015847.01.T01:intron 40.0%
! CTCTTCAACCTTGATGATCT+AGG + Chr3:75815981-75816000 None:intergenic 40.0%
! GCAGACATGCTTGTTAAAAC+TGG - Chr3:75816072-75816091 MsG0380015847.01.T01:five_prime_UTR 40.0%
! TCTCTGAGAGAGAAAGAGAA+TGG + Chr3:75814415-75814434 None:intergenic 40.0%
!! AGCTAGGATTTGGTGTTTGA+AGG - Chr3:75815545-75815564 MsG0380015847.01.T01:intron 40.0%
AGATCGAAAAGGACTCACCT+CGG + Chr3:75814547-75814566 None:intergenic 45.0%
CGACTTCATTTCACTCAACC+AGG + Chr3:75815407-75815426 None:intergenic 45.0%
GTCGCTTATAGAGAGAGAGT+AGG + Chr3:75814994-75815013 None:intergenic 45.0%
TTCTGTGTACTTCTCTCCCT+CGG + Chr3:75815654-75815673 None:intergenic 45.0%
AGATCACCCGAGATTATGCC+CGG - Chr3:75815701-75815720 MsG0380015847.01.T01:intron 50.0%
AGTGAAGAAGCTGTTGAGGC+CGG + Chr3:75815723-75815742 None:intergenic 50.0%
GATCGAAAAGGACTCACCTC+GGG + Chr3:75814546-75814565 None:intergenic 50.0%
GGTCAGTGAAGAAGCTGTTG+AGG + Chr3:75815727-75815746 None:intergenic 50.0%
GTGTTGGAGAACTTTGCCGA+GGG - Chr3:75815635-75815654 MsG0380015847.01.T01:intron 50.0%
TCTGCATCAACCCTGAAGTC+AGG - Chr3:75814701-75814720 MsG0380015847.01.T01:three_prime_UTR 50.0%
! AGTGTTGGAGAACTTTGCCG+AGG - Chr3:75815634-75815653 MsG0380015847.01.T01:intron 50.0%
! GGTATACCCTCTGTTTGCTG+CGG - Chr3:75814633-75814652 MsG0380015847.01.T01:three_prime_UTR 50.0%
AACAAGCAGTCTCGAGCTGC+AGG - Chr3:75815611-75815630 MsG0380015847.01.T01:intron 55.0%
CCACAGCATACACGCTGTTC+AGG + Chr3:75815880-75815899 None:intergenic 55.0%
CCTGAACAGCGTGTATGCTG+TGG - Chr3:75815877-75815896 MsG0380015847.01.T01:intron 55.0%
CTCCAACCGCAGCAAACAGA+GGG + Chr3:75814642-75814661 None:intergenic 55.0%
GTGAAGAAGCTGTTGAGGCC+GGG + Chr3:75815722-75815741 None:intergenic 55.0%
GTTGAGGCCGGGCATAATCT+CGG + Chr3:75815711-75815730 None:intergenic 55.0%
TATCCATGGCCACCAATCGC+TGG - Chr3:75814514-75814533 MsG0380015847.01.T01:three_prime_UTR 55.0%
TTGAGGCCGGGCATAATCTC+GGG + Chr3:75815710-75815729 None:intergenic 55.0%
! TACCCTCTGTTTGCTGCGGT+TGG - Chr3:75814637-75814656 MsG0380015847.01.T01:three_prime_UTR 55.0%
CAATCGCTGGATCAGACCCG+AGG - Chr3:75814527-75814546 MsG0380015847.01.T01:three_prime_UTR 60.0%
CTCGGGTCTGATCCAGCGAT+TGG + Chr3:75814529-75814548 None:intergenic 60.0%
CTGCGGTTGGAGCTGCTGTT+GGG - Chr3:75814650-75814669 MsG0380015847.01.T01:three_prime_UTR 60.0%
GCTCCAACCGCAGCAAACAG+AGG + Chr3:75814643-75814662 None:intergenic 60.0%
GGGTCTGATCCAGCGATTGG+TGG + Chr3:75814526-75814545 None:intergenic 60.0%
! GATCCAGCGATTGGTGGCCA+TGG + Chr3:75814520-75814539 None:intergenic 60.0%
! GTCTCGAGCTGCAGGAGTGT+TGG - Chr3:75815619-75815638 MsG0380015847.01.T01:intron 60.0%
GCTGCGGTTGGAGCTGCTGT+TGG - Chr3:75814649-75814668 MsG0380015847.01.T01:three_prime_UTR 65.0%
Chromosome Type Strat End Strand Name
Chr3 gene 75814364 75816160 75814364 ID=MsG0380015847.01;Name=MsG0380015847.01
Chr3 mRNA 75814364 75816160 75814364 ID=MsG0380015847.01.T01;Parent=MsG0380015847.01;Name=MsG0380015847.01.T01;_AED=0.49;_eAED=0.49;_QI=155|1|1|1|0|0|3|400|90
Chr3 exon 75814364 75814917 75814364 ID=MsG0380015847.01.T01:exon:1132;Parent=MsG0380015847.01.T01
Chr3 exon 75815802 75815890 75815802 ID=MsG0380015847.01.T01:exon:1131;Parent=MsG0380015847.01.T01
Chr3 exon 75815976 75816160 75815976 ID=MsG0380015847.01.T01:exon:1130;Parent=MsG0380015847.01.T01
Chr3 five_prime_UTR 75816006 75816160 75816006 ID=MsG0380015847.01.T01:five_prime_utr;Parent=MsG0380015847.01.T01
Chr3 CDS 75815976 75816005 75815976 ID=MsG0380015847.01.T01:cds;Parent=MsG0380015847.01.T01
Chr3 CDS 75815802 75815890 75815802 ID=MsG0380015847.01.T01:cds;Parent=MsG0380015847.01.T01
Chr3 CDS 75814764 75814917 75814764 ID=MsG0380015847.01.T01:cds;Parent=MsG0380015847.01.T01
Chr3 three_prime_UTR 75814364 75814763 75814364 ID=MsG0380015847.01.T01:three_prime_utr;Parent=MsG0380015847.01.T01
Gene Sequence

>MsG0380015847.01.T01

ATGGCCACCAATCGCTGGATCAGACCCGAGGTATACCCTCTGTTTGCTGCGGTTGGAGCTGCTGTTGGGATCTGTGCCTTTTCACTTGTTCGTAACATCTGCATCAACCCTGAAGTCAGGGTGAACAAGCAGTCTCGAGCTGCAGGAGTGTTGGAGAACTTTGCCGAGGGAGAGAAGTACACAGAACATTTGCTGAGGAAGTTTTCACGCAACAGATCACCCGAGATTATGCCCGGCCTCAACAGCTTCTTCACTGACCCAAGTCGCAACTAA

Protein sequence

>MsG0380015847.01.T01

MATNRWIRPEVYPLFAAVGAAVGICAFSLVRNICINPEVRVNKQSRAAGVLENFAEGEKYTEHLLRKFSRNRSPEIMPGLNSFFTDPSRN*